I would say that keeping a piece of paper to act as an index would help. Write the subject, and then the page number next to it, and then stick it at the back and add to it as needed. I like the idea of using tabs too, like the really cheapo ones that come in the packs of the same color with just a square of it in color and the rest of it is tape. As long as its acid free it won't do any harm to the book and you can freely move them around. Use them in the margin area, and don't stick more than two millimeters of them outside of the book, and they won't become an issue.
But like I said in your other post, you don't take notes and then organize them later on, the organization happens as you take them. If you're writing in a book, there's not much you can do except point out where all your markings are. You're basically going to end up rewriting them otherwise.
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